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Sample GSM3197090 Query DataSets for GSM3197090
Status Public on Jun 19, 2018
Title LLMGnc_082B
Sample type SRA
Source name Cell culture
Organism Lactococcus cremoris
Characteristics strain: NZ9000
accession: ASM14320v1
genotype: CisR overexpression
growth stage: Exponential
Treatment protocol cells were induced with nisin to overexpress (MS2-)LLMGnc_082 (CisR)
Growth protocol Bacterial cells were grown in M17 broth (containing 0,5% (w/v) glucose ) at 30°C
Extracted molecule total RNA
Extraction protocol Cell were lysed using glassbead and totRNA was isolated using phenol/chloroform and ethanol precipitation
Standard library preparation kit for IonProton
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
Description CisR overexpression
Data processing mapping of reads was done using: bowtie2 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 --local
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
RPKM values were normalized using the TMM (Trimmed Median Mean) method in T-REx (doi: 10.1186/s12864-015-1834-4)
Genome_build: Lactococcus lactis subsp. cremoris NZ9000, NC_017949.1, GI:389853198, Assembly: GCF_000143205.1, 12-AUG-2015
Supplementary_files_format_and_content: Tab delimited text file
Submission date Jun 18, 2018
Last update date Jun 19, 2018
Contact name Anne de Jong
Phone +31 50 363 2047
Organization name university of Groningen
Department Molecular Genetics
Street address Nijenborgh 7
City Groningen
ZIP/Postal code 9747 AG
Country Netherlands
Platform ID GPL24073
Series (1)
GSE115974 Target identification of the cold stress induced sRNA CisR in Lactococcus lactis
BioSample SAMN09445546
SRA SRX4232782

Supplementary file Size Download File type/resource
GSM3197090_LLMGnc_082B.01.rpkm.gz 69.6 Kb (ftp)(http) RPKM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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